exRNAdisease

General Information

Database ID:

exR0000023

RNA Name:

AATF

RNA Type:

mRNA

Chromosome:

chr17

Starnd:

Coordinate:

Start Site(bp):

36948954

End Site(bp):

37056871

External Links:

Disease Information

Disease Name:	Down Syndrome
Disease Category:	Congenital, Hereditary, and Neonatal Diseases and Abnormalities
MeSH ID:	D004314
Type:	Diseases Category/Congenital, Hereditary, and Neonatal Diseases and Abnormalities
Alias:	Syndrome, Down//Mongolism//47,XY,+21//Trisomy G//47,XX,+21//Down's Syndrome//Downs Syndrome//Syndrome, Down's//Trisomy 21//Trisomy 21, Mitotic Nondisjunction//Down Syndrome, Partial Trisomy 21//Partial Trisomy 21 Down Syndrome//Trisomy 21, Meiotic Nondisjunction

Expression Detail

GEO ID:	GSE16176
Description:	Expression profiles of amniotic fluid from human fetuses with Down syndrome and euploid controls
Experimental Design:	Disease vs Control
Case Disease Type:	Down Syndrome
Case Disease SubType:	NA
Case Sample:	Down Syndrome
Control Sample:	Normal
Number of Case:	7
Number of Control:	7
Number of Samples:	14

Regulatory Relationship

mRNA targets:

Gene Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
SSR1	chr6	7268306	7347446	-
RPS19	chr19	41860255	41872925	+
THY1	chr11	119417378	119424985	-
EIF3B	chr7	2354086	2380745	+
CD74	chr5	150400041	150412929	-
CASP2	chr7	143288215	143307696	+
BDH1	chr3	197509783	197573323	-
RNF113A	chrX	119870475	119871733	-
RTCA	chr1	100266207	100292769	+
AP002990.1	chr11	62559603	62591531	-
CKB	chr14	103519667	103522833	-
CLDN23	chr8	8701937	8704096	+
RPL8	chr8	144789765	144792587	-
VLDLR	chr9	2621787	2660056	+
ACTB	chr7	5527148	5563784	-
MT-CO3	chrMT	9207	9990	+
RPS6	chr9	19375715	19380236	-
NIPA2	chr15	22838641	22868384	+
UBA52	chr19	18571730	18577550	+
DYNC1H1	chr14	101964573	102056443	+
UBALD2	chr17	76265348	76271298	+
LSM1	chr8	38163335	38176730	-
CIC	chr19	42268537	42295797	+
PAQR3	chr4	78887127	78939438	-
CCNA2	chr4	121816444	121823933	-
TMEM258	chr11	61768501	61792802	-
ACTR1B	chr2	97655939	97664044	-
CIT	chr12	119685791	119877320	-
FAN1	chr15	30890559	30943108	+
SRGN	chr10	69088103	69104805	+

miRNA targets:

miRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
hsa-miR-4492	chr11	118910765	118910781	+

circRNA targets:

lncRNA targets:

lncRNA Symbol	Chromosome	Start Site(bp)	End Site(bp)	Strand
AL355987.4	chr9	136799223	136810042	+
NAALADL2-AS2	chr3	175234861	175271096	-
SNHG1	chr11	62851984	62855953	-
XIST	chrX	73820649	73852723	-

Display:

Experiment Detail

GEO ID:	GSE16176
Sample Source:	Amniotic Fluid
Source Fraction:	Supernatant
Platform:	GPL570
Method:	Microarray
Num of detected RNA Type:	1
Num of detected RNAs of this Type:	17063
Sample treatment protocol:	NA
RNA Extract protocol:	RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer's protocol (QIAGEN, Valencia, CA). RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).
RNA library preparation protocol:	biotin Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

Reference

PMID:	19474297
Title:	Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses
Author:	Slonim DK, Koide K, Johnson KL, Tantravahi U, Cowan JM, Jarrah Z, Bianchi DW
Journal:	Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9425-9.
Description:	To characterize the differences between second trimester Down syndrome (DS) and euploid fetuses, we used Affymetrix microarrays to compare gene expression in uncultured amniotic fluid supernatant samples.